Ben Soares [Mon, 18 Mar 2019 16:53:33 +0000 (16:53 +0000)]
JAL-3130 removing no longer needed JRE (going to use adoptopenjdk jre11)
Ben Soares [Mon, 18 Mar 2019 16:50:43 +0000 (16:50 +0000)]
JAL-3130 Removing accidentally committed tmp dir
Ben Soares [Mon, 18 Mar 2019 15:17:27 +0000 (15:17 +0000)]
JAL-3130 Some automatically fixed deprecated calls. Mostly constructors converted to .valueOf() to use a final static version. See utils/deprecation_auto_fixes.sh
Ben Soares [Thu, 7 Mar 2019 15:29:38 +0000 (15:29 +0000)]
JAL-3130 deprecation change preparation
Ben Soares [Tue, 18 Dec 2018 14:14:57 +0000 (14:14 +0000)]
JAL-3130 added a javac helper script too (like the java helper script)
Ben Soares [Mon, 17 Dec 2018 10:37:13 +0000 (10:37 +0000)]
JAL-3130 java bash wrapper to choose which java to run (if this is first in path) -- useful when you want javac and java to be from different JAVA_HOME when running ant
Ben Soares [Mon, 17 Dec 2018 10:34:21 +0000 (10:34 +0000)]
JAL-3130 Some fixes to ant build xml, and the modules list file creation (to remove trailing newline) so it can be used with module-less AdoptOpenJDK barebones JRE
Ben Soares [Fri, 14 Dec 2018 10:10:39 +0000 (10:10 +0000)]
JAL-3130 single class testing on CLI with ant [ -Dclass.name=path/from/classpath/to/Test.class ], and 'fixed' some other tests [that I broke]
Ben Soares [Thu, 13 Dec 2018 14:50:02 +0000 (14:50 +0000)]
JAL-3130 Fixing a few more tests that pass on a Mac but not on linux (e.g. jv-bamboo)
Ben Soares [Thu, 13 Dec 2018 12:12:21 +0000 (12:12 +0000)]
JAL-3130 Use non-deprecated check for Mac CMD key press
Ben Soares [Thu, 13 Dec 2018 09:27:46 +0000 (09:27 +0000)]
JAL-3130 Attempting to fix 8 tests that pass on a Mac but not on linux (e.g. jv-bamboo)
Ben Soares [Tue, 11 Dec 2018 17:09:51 +0000 (17:09 +0000)]
JAL-3130 Turns out Quit/About/Preferences handlers are Mac specific, d'oh. Moved build.xml to build-j11.xml
Ben Soares [Mon, 10 Dec 2018 16:59:56 +0000 (16:59 +0000)]
JAL-3130 another tweak for bamboo to add the JDK jmods to --module-path
Ben Soares [Mon, 10 Dec 2018 15:59:59 +0000 (15:59 +0000)]
JAL-3130 build.xml tweaks for clover-3.4.1
Ben Soares [Mon, 10 Dec 2018 11:01:49 +0000 (11:01 +0000)]
JAL-3130 tweaked build.xml to do java 11 bytecode compiling[git branchgit branch]. updated getJavaVersion and added showJDKVersion in utils.
Ben Soares [Fri, 7 Dec 2018 10:26:10 +0000 (10:26 +0000)]
JAL-3130 Some re-reorganisation for build process
Ben Soares [Thu, 6 Dec 2018 16:29:24 +0000 (16:29 +0000)]
JAL-3130 incorporating feature/JAL-3063jaxbNoCastor and new script utils/jdeps_jlink_all.sh which works out module dependencies (not as straightforward as it should be) and makes a java 11 JRE
Ben Soares [Mon, 3 Dec 2018 15:18:17 +0000 (15:18 +0000)]
JAL-3130 de-multi-release-jar.sh Script to make multi-release jar file single release.
Ben Soares [Mon, 3 Dec 2018 12:20:57 +0000 (12:20 +0000)]
JAL-3130 Added flagged runtime 'Reflection' check on Java9 Quit/About/Preferences Handlers
Ben Soares [Fri, 30 Nov 2018 16:54:00 +0000 (16:54 +0000)]
JAL-3130 refactored a lot of this. See the JAVA-11-README
Ben Soares [Mon, 19 Nov 2018 16:20:14 +0000 (16:20 +0000)]
JAL-1988 JAL-3130 New jlinked JRE in jalview_java2 with modules. Still needs jaxws-2.3.1/lib in the classpath, but no modulepath needed
Ben Soares [Fri, 9 Nov 2018 16:44:32 +0000 (16:44 +0000)]
JAL-1988 This fixes the Quit response when user cancels the quit
Ben Soares [Thu, 8 Nov 2018 16:53:42 +0000 (16:53 +0000)]
JAL-1988 JAL-3130 Now we're in Java 11 land, using jdeps and jlink have made a pared down Java 11 (44MB) in jalview_java. Run with './jalview_java/bin/java -cp "classes:lib/*:j11lib/*" jalview.bin.Jalview'.
Ben Soares [Thu, 8 Nov 2018 14:46:17 +0000 (14:46 +0000)]
JAL-1988 tidying, plus don't add Preferences to Tools menu on a Mac\!
Ben Soares [Thu, 8 Nov 2018 14:28:10 +0000 (14:28 +0000)]
JAL-1988 JAVA 11 enabled version with Quit, Preferences and About handlers enabled for Mac. Run with openjdk-11 and 'java -classpath "classes:lib/*:j11lib/*" jalview.bin.Jalview'
Ben Soares [Mon, 5 Nov 2018 16:47:41 +0000 (16:47 +0000)]
JAL-1988 Investigating...
gmungoc [Thu, 20 Sep 2018 11:23:14 +0000 (12:23 +0100)]
JAL-2843 tweaks to help text for filters
gmungoc [Thu, 20 Sep 2018 10:54:31 +0000 (11:54 +0100)]
JAL-2843 help text for colour by attribute, feature filters
Jim Procter [Wed, 19 Sep 2018 14:45:29 +0000 (15:45 +0100)]
Merge branch 'bug/JAL-3120restoreFeatureColour' into develop
gmungoc [Wed, 19 Sep 2018 13:59:44 +0000 (14:59 +0100)]
JAL-3120 preserve plain colour value when changing to Colour by Label
gmungoc [Wed, 19 Sep 2018 12:44:58 +0000 (13:44 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 19 Sep 2018 11:39:17 +0000 (12:39 +0100)]
Merge branch 'cherrypick/JAL-2808_notabs' into develop
Jim Procter [Thu, 5 Jul 2018 13:38:42 +0000 (14:38 +0100)]
JAL-2808 JAL-3026 deleted all commented out tab code from the dialog
Omitted dialog refactoring from JAL-3058
gmungoc [Thu, 5 Jul 2018 13:27:44 +0000 (14:27 +0100)]
JAL-2808 JAL-3032 drop tabbed layout for Colours and Filters
Jim Procter [Tue, 18 Sep 2018 14:01:56 +0000 (15:01 +0100)]
JAL-2865 release notes
gmungoc [Wed, 12 Sep 2018 15:30:52 +0000 (16:30 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 12 Sep 2018 15:20:51 +0000 (16:20 +0100)]
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop
gmungoc [Wed, 12 Sep 2018 11:27:21 +0000 (12:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 12 Sep 2018 10:59:39 +0000 (11:59 +0100)]
JAL-1551 reinstated Save actions
Jim Procter [Tue, 11 Sep 2018 15:06:03 +0000 (16:06 +0100)]
JAL-3112 increased TEST_TIMEOUT to 9000ms - needed after inclusion discovered class path entries
Jim Procter [Tue, 11 Sep 2018 15:05:02 +0000 (16:05 +0100)]
JAL-3112 Use classgraph to reconstruct the classpath for launching Jalview
Jim Procter [Tue, 11 Sep 2018 13:05:00 +0000 (14:05 +0100)]
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop
Jim Procter [Tue, 11 Sep 2018 13:03:50 +0000 (14:03 +0100)]
JAL-3111 drop hts-1.33 as a dependency (in favour of htsjdk-2.12)
Jim Procter [Tue, 11 Sep 2018 12:56:41 +0000 (13:56 +0100)]
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop
Jim Procter [Tue, 11 Sep 2018 12:31:09 +0000 (13:31 +0100)]
Merge branch 'releases/Release_2_11_Branch' into merge/JAL-3091_develop_211
Jim Procter [Tue, 11 Sep 2018 12:29:37 +0000 (13:29 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch
JAL-3091 bring 2.11 onto release 2.10.5 to simplify merge
Jim Procter [Sun, 9 Sep 2018 13:14:52 +0000 (14:14 +0100)]
JAL-3091 changed release date to 10th September - tweaked release notes.
Jim Procter [Sun, 9 Sep 2018 13:04:28 +0000 (14:04 +0100)]
JAL-3106 normalise extension before checking if it is '.jar' when constructing fileformat/extension name index
Jim Procter [Fri, 7 Sep 2018 14:05:27 +0000 (15:05 +0100)]
JAL-3107 update any group associated annotation rows when a new group is created
Jim Procter [Fri, 7 Sep 2018 13:51:13 +0000 (14:51 +0100)]
JAL-2988 JAL-2968 renamed patched VAqua5 to VAqua5-patch.jar and documented patch along with instructions for rebuilding the jar
Jim Procter [Fri, 7 Sep 2018 13:24:20 +0000 (14:24 +0100)]
JAL-2988 if selected file is null (On Java 10/OSX - happens if user has entered text after selecting a file), try and get the filename from the UI. If no file can be gotten, cancel the save operation
Jim Procter [Fri, 7 Sep 2018 13:23:16 +0000 (14:23 +0100)]
JAL-2988 workaround: overload getSelectedFile() because calling setSelectedFile(..) results in getSelectedFile()==null on OSX/Java 10/VAqua4/5.
Jim Procter [Fri, 7 Sep 2018 13:19:28 +0000 (14:19 +0100)]
JAL-3106 use .jvp as default
Jim Procter [Fri, 7 Sep 2018 11:24:10 +0000 (12:24 +0100)]
JAL-3105 fix for focus transfer after window closed on OSX
Jim Procter [Thu, 6 Sep 2018 19:51:47 +0000 (20:51 +0100)]
JAL-3091 code committed in error (failed patch for JAL-2854)
Jim Procter [Thu, 6 Sep 2018 19:41:29 +0000 (20:41 +0100)]
JAL-3091 release notes for JAL-3104
Jim Procter [Thu, 6 Sep 2018 19:37:06 +0000 (20:37 +0100)]
JAL-3105 reallocate quality and consensus annotation rows so old values aren’t rendered when alignments become shorter
Jim Procter [Thu, 6 Sep 2018 19:33:43 +0000 (20:33 +0100)]
JAL-2854 compute visible annotation panel height and provide it directly to via Scrollable interface
Jim Procter [Wed, 5 Sep 2018 17:12:14 +0000 (18:12 +0100)]
JAL-3065 don’t quote class path args for Runtime.exec java launch command (needs to be ported to 2.11)
Jim Procter [Wed, 5 Sep 2018 16:58:24 +0000 (17:58 +0100)]
JAL-3091 update whats new!
Jim Procter [Wed, 5 Sep 2018 14:14:08 +0000 (15:14 +0100)]
JAL-3091 update Java 10 known issues/workarounds in whats new
Jim Procter [Wed, 5 Sep 2018 13:59:24 +0000 (14:59 +0100)]
JAL-3091 known defect in whats new for Java 10 issues: JAL-3103 JAL-3102
Jim Procter [Wed, 5 Sep 2018 13:34:25 +0000 (14:34 +0100)]
JAL-3091 add Ben Soares to authors list and switch ordering of Toch and Kira (since Kira left after Toch).
Jim Procter [Wed, 5 Sep 2018 13:28:50 +0000 (14:28 +0100)]
JAL-3091 release notes for updated memory settings
Jim Procter [Wed, 5 Sep 2018 12:59:51 +0000 (13:59 +0100)]
JAL-3091 release notes
Jim Procter [Wed, 5 Sep 2018 12:57:15 +0000 (13:57 +0100)]
JAL-3101 increase default heap size in IA and JNLP generation, and generate a jalview_256MB.jnlp file for backwards compatibility
Jim Procter [Wed, 5 Sep 2018 10:06:54 +0000 (11:06 +0100)]
Merge branch 'patch/VAqua_saveload_update_JAL-2988' into releases/Release_2_10_5_Branch
Jim Procter [Wed, 5 Sep 2018 10:06:00 +0000 (11:06 +0100)]
JAL-2988 update InstallAnywhere install dependencies for VAqua5
Jim Procter [Wed, 5 Sep 2018 09:42:11 +0000 (10:42 +0100)]
Merge branch 'bug/JAL-3076ensemblGeneId' into develop
Jim Procter [Wed, 5 Sep 2018 08:04:19 +0000 (09:04 +0100)]
JAL-3091 release date set for Thursday 6th September
Jim Procter [Wed, 5 Sep 2018 08:03:37 +0000 (09:03 +0100)]
Merge branch 'bug/JAL-3065_DH_keyPair_Exception_nogroovysettings' into releases/Release_2_10_5_Branch
Jim Procter [Wed, 5 Sep 2018 08:01:50 +0000 (09:01 +0100)]
JAL-3065 - amended commit
4906697ab6e5a79fbce3baae89f7f64178c9a739 to exclude .settings/..groovy
Added notes to the instructions, also adjusted the jalviewDesktopRunner
test to lookup OS and use ';' or ':' accordingly.
All the CommandLineOperations tests failed on my (hastily set up) linux
box, so I'm committing and will test on MacOS too.
Jim Procter [Tue, 4 Sep 2018 12:02:44 +0000 (13:02 +0100)]
JAL-3091 JAL-2988 release notes re Java 10 and OSX
Jim Procter [Mon, 3 Sep 2018 18:58:18 +0000 (19:58 +0100)]
Merge branch 'patch/VAqua_saveload_update_JAL-2988' into releases/Release_2_10_5_Branch
Jim Procter [Mon, 3 Sep 2018 18:48:42 +0000 (19:48 +0100)]
Merge branch 'releases/Release_2_10_5_Branch' of source.jalview.org/git/jalview into releases/Release_2_10_5_Branch
Jim Procter [Mon, 3 Sep 2018 15:45:51 +0000 (16:45 +0100)]
JAL-3091 -Dnosign to disable jar signing phase of build
Jim Procter [Mon, 3 Sep 2018 15:45:51 +0000 (16:45 +0100)]
JAL-3091 -Dnosign to disable jar signing phase of build
Jim Procter [Mon, 3 Sep 2018 15:45:23 +0000 (16:45 +0100)]
JAL-3091 release notes and whats new !
gmungoc [Mon, 3 Sep 2018 14:04:14 +0000 (15:04 +0100)]
Merge branch 'trialMerge' into releases/Release_2_10_5_Branch
gmungoc [Fri, 10 Aug 2018 09:59:42 +0000 (10:59 +0100)]
JAL-3076 fetch Ensembl sequence as JSON instead of Fasta
Conflicts:
src/jalview/ext/ensembl/EnsemblInfo.java
src/jalview/ext/ensembl/EnsemblMap.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
Jim Procter [Mon, 3 Sep 2018 13:26:54 +0000 (14:26 +0100)]
JAL-3065 release notes
Jim Procter [Mon, 3 Sep 2018 13:22:58 +0000 (14:22 +0100)]
Merge branch 'bug/JAL-3065_DH_keyPair_Exception' into releases/Release_2_10_5_Branch
Jim Procter [Mon, 3 Sep 2018 13:03:54 +0000 (14:03 +0100)]
JAL-3076 clarify javadoc handling single sequence response for Ensembl REST sequence_id endpoint
Jim Procter [Mon, 3 Sep 2018 12:33:35 +0000 (13:33 +0100)]
JAL-3087 release notes
Jim Procter [Fri, 31 Aug 2018 15:08:32 +0000 (16:08 +0100)]
JAL-3095 account for sequence start when highlighting selections in trimmed VARNA model
Jim Procter [Fri, 31 Aug 2018 15:03:42 +0000 (16:03 +0100)]
JAL-3053 JAL-3061 JAL-3095 release notes
Jim Procter [Fri, 31 Aug 2018 14:04:32 +0000 (15:04 +0100)]
Merge branch 'bug/JAL-3061_RNA_secondary_structure_annotation_gap_character' into releases/Release_2_10_5_Branch
Jim Procter [Fri, 31 Aug 2018 11:12:46 +0000 (12:12 +0100)]
Merge branch 'releases/Release_2_10_5_Branch' of source.jalview.org/git/jalview into releases/Release_2_10_5_Branch
Jim Procter [Fri, 31 Aug 2018 11:12:20 +0000 (12:12 +0100)]
JAL-3095 release notes
Jim Procter [Fri, 31 Aug 2018 11:10:26 +0000 (12:10 +0100)]
java doc and fix for JAL-3095 - region of trimmed RNA model to highlight is indexed relative to SeuqenceI.getStart()
gmungoc [Fri, 31 Aug 2018 10:49:00 +0000 (11:49 +0100)]
JAL-3003 remove redundant call to drawSelectionGroup
Jim Procter [Thu, 30 Aug 2018 15:34:58 +0000 (16:34 +0100)]
JAL-3092 release notes
Jim Procter [Thu, 30 Aug 2018 15:31:37 +0000 (16:31 +0100)]
JAL-3092 make sure base pair counter is always moved in loop that computes the helix count for a strand of RNA secondary structure
Jim Procter [Wed, 29 Aug 2018 09:17:25 +0000 (10:17 +0100)]
JAL-3091 release notes for JAL-3003 JAL-3059
Jim Procter [Tue, 28 Aug 2018 16:11:48 +0000 (17:11 +0100)]
JAL-3003 different coloured borders in demo annotation file
gmungoc [Thu, 23 Aug 2018 12:28:52 +0000 (13:28 +0100)]
JAL-3059 use correct border colour for groups
gmungoc [Thu, 23 Aug 2018 12:27:10 +0000 (13:27 +0100)]
JAL-3003 draw selection group outline on main graphics context
Jim Procter [Tue, 28 Aug 2018 15:28:38 +0000 (16:28 +0100)]
JAL-247 release notes
gmungoc [Mon, 27 Aug 2018 09:19:28 +0000 (10:19 +0100)]
JAL-247 comment to clarify wrapped print algorithm
gmungoc [Fri, 24 Aug 2018 15:16:08 +0000 (16:16 +0100)]
JAL-247 print/export wrapped uses common code to draw seq ids and
annotation labels
git://source.jalview.org / jalview.git / log